383da828477aad2b3c6053880a64fdbfc2a00cd9 max Thu Mar 19 02:30:41 2026 -0700 Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/human/topmed.html src/hg/makeDb/trackDb/human/topmed.html index 4d0fcf3d3b5..68a1865ef8e 100644 --- src/hg/makeDb/trackDb/human/topmed.html +++ src/hg/makeDb/trackDb/human/topmed.html @@ -4,31 +4,31 @@ Medicine) is a program launched by the U.S. National Heart, Lung, and Blood Institute that integrates whole-genome sequencing with molecular, clinical, and environmental data from large, well-phenotyped cohorts. Its goal is to uncover the biological mechanisms underlying heart, lung, blood, and sleep disorders to advance precision medicine and improve population health. Freeze 10 contains 868,581,653 variants from 150,899 whole genomes. </p> <h2>Data Access</h2> <p> The data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. For programmatic access, our <a href="https://api.genome.ucsc.edu">REST API</a> can be used; the track name is <em>topmed</em>. For bulk download, the VCF file can be obtained from -<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/varFreqs/" target="_blank">our download server</a>. +<a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/varFreqs/" target="_blank">our download server</a>. </p> <p> VCFs with summarized allele frequencies are also available from the <a href="https://bravo.sph.umich.edu/" target="_blank">TOPMED BRAVO website</a>. They require a login. The VCFs were downloaded from <a href="https://bravo.sph.umich.edu/terms.html" target="_blank">BRAVO</a>. </p> <h2>Methods</h2> <p> TOPMed whole genome sequencing was performed at multiple NHLBI-funded sequencing centers using PCR-free library preparation with 150 bp paired-end reads on Illumina short-read platforms, targeting ≥30x mean coverage. Reads were aligned to the GRCh38 reference genome (hs38DH, including decoy sequences) using BWA-MEM, followed by duplicate marking with Picard MarkDuplicates and base quality score recalibration (BQSR) with GATK. Variant calling @@ -36,18 +36,18 @@ Genetics, University of Michigan), comprising: (1) per-sample candidate variant detection with <code>vt discover2</code> and normalization with <code>vt normalize</code>; (2) cross-sample variant site consolidation using <code>cramore vcf-merge-candidate-variants</code>; (3) joint genotyping across all samples; and (4) variant filtering using a Support Vector Machine (SVM) classifier (libsvm) trained on positive labels derived from HapMap 3.3 and 1000 Genomes Omni2.5 array sites, and negative labels derived from Mendelian-inconsistent variants identified within the cohort's pedigree structure using <code>vt milk-filter</code>. Sample-level quality control included estimation of DNA contamination, genetic ancestry, and biological sex using <code>cramore cram-verify-bam</code> (verifyBamID2) and relative X/Y chromosomal depth. Full methods for TOPMed freeze 10 are available on the <a href="https://topmed.nhlbi.nih.gov/topmed-whole-genome-sequencing-methods-freeze-10" target="_blank">TOPMed WGS Methods page</a>. </p> <p> -We provide documentation that indicates how all source files of the varFreqs track were converted in the <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/varFreqs.txt" target=_blank>makeDoc file</a> of the track. -For some tracks, python scripts were necessary and are also available from <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/scripts/varFreqs" target=_blank>Github</a>. +We provide documentation that indicates how all source files of the varFreqs track were converted in the <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/varFreqs.txt" target="_blank">makeDoc file</a> of the track. +For some tracks, python scripts were necessary and are also available from <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/scripts/varFreqs" target="_blank">GitHub</a>. </p>